Ryan Wick @rrwick
No longer active here. Find me on Bluesky: https://t.co/1mPtWVlnli rrwick.github.io Melbourne Joined August 2013-
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To make producing soft core alignments easier, we developed Core-SNP-filter, a simple and efficient tool to process SNP alignments with user-defined thresholds. github.com/rrwick/Core-SN… (4/4)
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And the benefits grow with dataset size! A 100% strict core may work fine for small datasets (e.g. ~10 genomes) but is devastating for very large ones (e.g. 1000+ genomes). A 95% soft core works well across all dataset sizes. (3/4)
Do you make core genome alignments for phylogenomics? @monaltaouk and I explored how including sites with some missing data (a soft core) can improve analysis, especially for large datasets. microbiologyresearch.org/content/journa… (1/4)
@krannich479 You can certainly give it a try, but linear sequences can be challenging for Autocycler at the moment (a focus for future development), so if your viral genome is not circular, it may not be a great fit.
New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autocyc… (1/5)
Autocycler is still new and evolving. I'll continue to improve it based on your feedback. A big thank you to the alpha testers who gave me feedback before this release! Give it a try and share your thoughts. (5/5)
However, Autocycler still allows users to manually intervene when they would like to. So it aims for the best of both worlds: either hands-off automated assemblies or hands-on curated assemblies, as the user sees fit. (4/5)
Just had my first experience with CycloneSEQ data and shared my findings in this blog post: rrwick.github.io/2024/12/17/cyc… How does CycloneSEQ compare to @nanopore? I looked at both read-level and consensus-level accuracy. Check it out!
Ryan Wick retweeted
If you want to try out the new --bacteria Medaka polishing option after reading Ryan's thoughts in his latest blogpost, the newest Hybacter v0.10.0 release now includes it as the default github.com/gbouras13/hybr…
A little bit overdue, but here are my thoughts on @nanopore's recent release of Medaka: rrwick.github.io/2024/10/17/med…
A little bit overdue, but here are my thoughts on @nanopore's recent release of Medaka: rrwick.github.io/2024/10/17/med…
Ryan Wick retweeted
Excited to share this preprint where we’ve used genomic analysis of >3000 genomes to study Klebsiella pneumoniae in a One Health perspective 🦠🔬👩💻#OneHealth #KLEBGAP #KlebClub @IrenLohr @DrKatHolt @NORKLEBNET
A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events ... biorxiv.org/cgi/content/sh… #biorxiv_micrbio
Our OnION sequencing computer now has a little sibling: Spring OnION! Short post with some stats and benchmarks: rrwick.github.io/2024/08/16/spr…
@martinalexsmith @nanopore If you're assembling hac reads, then make sure to run Medaka. I've found it's much more beneficial for hac-based assemblies than for sup-based assemblies.
I finally got around to testing HERRO (github.com/lbcb-sci/herro), the new @nanopore read correction algorithm which takes simplex ONT reads to PacBio-HiFi-level accuracy. I was impressed! Findings are on my blog in a two-part post: rrwick.github.io/2024/07/26/her… rrwick.github.io/2024/07/31/her…
Ryan Wick retweeted
How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: doi.org/10.1099/mgen.0…
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